view covacs_mpileup.xml @ 1:c6eea29aa0ab draft default tip

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 <tool id="covacs_mpileup" name="covacs_mpileup" version="1.9">
  <description>samtools mpileup wrapper for covacs</description>
  <macros>
	<import>bed_macros.xml</import>
	<import>covacs_macros.xml</import>
  </macros>
  <requirements>
  	<requirement type="package" version="1.9" >samtools</requirement>
  </requirements>
  <command>
    <![CDATA[


       samtools mpileup 
	 -C $adjust 
	#if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
	  -l $bed_source.bed_history
	  #end if
  	  #if $bed_source.bed_source_selector == "cached"
   	  -l $bed_source.bed_cached.fields.path
    	 #end if

	-d $depth
	-q $MappingQuality
	-Q $BaseQuality
	#if $reference_source.reference_source_selector == "cached"
                -f $reference_source.ref_file.fields.path
        #end if
	
	#if $reference_source.reference_source_selector == "history"
	
         -f $reference_source.ref_file_h
	
	#end if

	$input1 -A -o $output 2>$log

	



	]]>
  </command>
  <inputs>
    <param format="bam" name="input1" label="bam-input" type="data" optional="true" />
    <param name="adjust" type="integer" optional="true" value="50" help="adjust mapping quality"/>
    <expand macro="bed_loc"/>
    <param name="depth" type="integer" optional="true" value="100000" help="max per-file depth" />
    <param name="MappingQuality" type="integer" optional="true" value="0" help="skip alignments with mapQ smaller than INT" />
    <param name="BaseQuality" type="integer" optional="true" value="0" help="skip bases with baseQ/BAQ smaller than INT" />
    <expand macro="reference_loc"/>
  </inputs>
  <outputs>
    <data format="pileup" name="output" label="mpileup on ${on_string}"/>
    <data format="txt" name="log" label="mpileup on ${on_string}:log"/>
  </outputs>
  <help>
**more information** at http://www.htslib.org/doc/samtools-1.2.html

**Implemented options** samtools mpileup
  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)
  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]
  -d, --max-depth INT     max per-file depth; avoids excessive memory usage [8000]
  -f, --fasta-ref FILE    faidx indexed reference sequence file
  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)
  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [0]
  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [13]
**fixed option**
  -A, --count-orphans     do not discard anomalous read pairs

  </help>
  <citations>
        <citation type="doi">10.1186/s12864-018-4508-1</citation>
  </citations>
</tool>